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- PDB-1i85: CRYSTAL STRUCTURE OF THE CTLA-4/B7-2 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1i85
TitleCRYSTAL STRUCTURE OF THE CTLA-4/B7-2 COMPLEX
Components
  • CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED PROTEIN 4
  • T LYMPHOCYTE ACTIVATION ANTIGEN CD86
KeywordsIMMUNE SYSTEM / Ig V-type domain
Function / homology
Function and homology information


positive regulation of lymphotoxin A production / protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / positive regulation of T-helper 2 cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / Co-stimulation by CD28 / CD28 dependent Vav1 pathway / positive regulation of immunoglobulin production / Co-inhibition by CTLA4 ...positive regulation of lymphotoxin A production / protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / positive regulation of T-helper 2 cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / Co-stimulation by CD28 / CD28 dependent Vav1 pathway / positive regulation of immunoglobulin production / Co-inhibition by CTLA4 / negative regulation of B cell proliferation / Interleukin-10 signaling / positive regulation of interleukin-4 production / B cell activation / CD28 dependent PI3K/Akt signaling / positive regulation of T cell proliferation / coreceptor activity / negative regulation of T cell proliferation / T cell costimulation / positive regulation of interleukin-2 production / T cell activation / B cell receptor signaling pathway / positive regulation of non-canonical NF-kappaB signal transduction / centriolar satellite / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / T cell receptor signaling pathway / signaling receptor activity / virus receptor activity / cellular response to lipopolysaccharide / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / adaptive immune response / cell surface receptor signaling pathway / immune response / positive regulation of apoptotic process / receptor ligand activity / external side of plasma membrane / positive regulation of cell population proliferation / DNA damage response / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / cell surface / Golgi apparatus / extracellular exosome / plasma membrane
Similarity search - Function
CD86, IgV domain / Cytotoxic T-lymphocyte antigen 4 / Cytotoxic T-lymphocyte protein 4/CD28 / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...CD86, IgV domain / Cytotoxic T-lymphocyte antigen 4 / Cytotoxic T-lymphocyte protein 4/CD28 / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cytotoxic T-lymphocyte protein 4 / T-lymphocyte activation antigen CD86
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSchwartz, J.-C.D. / Zhang, X. / Fedorov, A.A. / Nathenson, S.G. / Almo, S.C.
CitationJournal: Nature / Year: 2001
Title: Structural basis for co-stimulation by the human CTLA-4/B7-2 complex.
Authors: Schwartz, J.C. / Zhang, X. / Fedorov, A.A. / Nathenson, S.G. / Almo, S.C.
History
DepositionMar 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T LYMPHOCYTE ACTIVATION ANTIGEN CD86
B: T LYMPHOCYTE ACTIVATION ANTIGEN CD86
C: CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED PROTEIN 4
D: CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED PROTEIN 4


Theoretical massNumber of molelcules
Total (without water)52,7204
Polymers52,7204
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.85, 54.56, 103.09
Angle α, β, γ (deg.)90.00, 91.63, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe CTLA-4 homodimer is generated by Chain D and the translatonal symmetry mate of chain C (apply the operator x,y,z+1 to Chain C) / The repeating arrangement of CTLA-4 and B7-2 dimers is generated by applying the translational symmetry operation (x,y,z+/-N; where N ranges over all integers) to all chains in the asymmetric unit

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Components

#1: Antibody T LYMPHOCYTE ACTIVATION ANTIGEN CD86 / B7-2


Mass: 12849.631 Da / Num. of mol.: 2 / Fragment: IG V-TYPE (RECEPTOR BINDING) DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD86 / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P42081
#2: Protein CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED PROTEIN 4 / CTLA-4


Mass: 13510.340 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTLA4 / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P16410
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG20K, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 mg/mlprotein1drop
218 %PEG200001reservoir
3100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2000
RadiationMonochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→25 Å / Num. all: 7080 / Num. obs: 7080 / % possible obs: 78.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 6.6
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.2 / % possible all: 79.4
Reflection shell
*PLUS
% possible obs: 79.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→10 Å / Cross valid method: THROUGHOUT / σ(F): 1.2 / σ(I): 1.4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3 606 10 %RANDOM
Rwork0.217 ---
all-8655 --
obs-6516 --
Displacement parametersBiso mean: 20.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.69 Å
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3515 0 0 0 3515
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.97
LS refinement shellResolution: 3.2→3.31 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.419 61 10 %
Rwork0.372 415 -
obs--56.3 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.97

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